Hello,
Sorry in advanced if this sounds like a silly question.
We use a piece of software that runs on our Windows Server and previously when we receive a new certificate we would import it into IIS and then login to the software and select the new certificate.
We want to move to Lets Encypt, I understand that the certificates only last 90 days, does this mean every 90 days I need to go into our software and select a new certificate or does the existing certificate get extended?
Thanks!
Certificates, once issued, are immutable. All “renewals” are really just new certificates for the same domains, in reality. You, or some automated process, would need to apply them. There are several different pieces of software for Windows to interact with Let’s Encrypt, some of which I believe can renew and apply the certificates in IIS automatically.
See the page https://letsencrypt.org/docs/client-options/ on the Let’s Encrypt website for a list of clients, obviously the clients which interest you the most are probably in the “Windows / IIS” section 
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